Complete sequencing of 62 mitochondrial DNAs (mtDNAs) belonging (or very closely related) to haplogroup H revealed that this mtDNA haplogroup—by far the most common in Europe—is subdivided into numerous subhaplogroups, with at least 15 of them (H1–H15) identifiable by characteristic mutations. All the haplogroup H mtDNAs found in 5,743 subjects from 43 populations were then screened for diagnostic markers of subhaplogroups H1 and H3. This survey showed that both subhaplogroups display frequency peaks, centered in Iberia and surrounding areas, with distributions declining toward the northeast and southeast—a pattern extremely similar to that previously reported for mtDNA haplogroup V. Furthermore, the coalescence ages of H1 and H3 (∼11,000 years) are close to that previously reported for V. These findings have major implications for the origin of Europeans, since they attest that the Franco-Cantabrian refuge area was indeed the source of late-glacial expansions of hunter-gatherers that repopulated much of Central and Northern Europe from ∼15,000 years ago. This has also some implications for disease studies. For instance, the high occurrence of H1 and H3 in Iberia led us to re-evaluate the haplogroup distribution in 50 Spanish families affected by nonsyndromic sensorineural deafness due to the A1555G mutation. The survey revealed that the previously reported excess of H among these families is caused entirely by H3 and is due to a major, probably nonrecent, founder event.

For most of human evolution, and particularly during the recent process of diffusion from Africa to the other continents, the relatively fast evolution of human mitochondrial DNAs (mtDNAs) has occurred in a context of small founding populations. Thus, founder events and genetic drift have played a major role in shaping haplotype frequencies, giving rise to haplogroups and subhaplogroups that are often restricted to specific geographic areas and/or population groups. In Europe, with the exception of U5 and V, which most likely arose in situ, all mtDNA haplogroups (H, I, J, K, T, U2e, U3, U4, X, and W) are most likely of Middle Eastern origin and were introduced by either the protocolonization ~45–40 thousand years ago (kya), by later arrivals in the Middle/Late Upper Paleolithic, Neolithic dispersals, or by more recent contacts (Torroni et al. 1998; Richards et al. 2000). For some haplogroups, particularly the more common ones, multiple chronologically distinct arrivals to Europe are extremely likely. In addition, the genetic landscape of Europe has probably been further confounded by the major climatic changes that have occurred since the arrival of the first modern humans. In particular, the early Paleolithic populations of Northern and Central Europe either became extinct or retreated to the south during the Last Glacial Maximum (LGM) ~20 kya, and there was a gradual repeopling from southern refuge areas only when climatic conditions improved, from ~15 kya. This scenario is supported not only by recent work on archaeological dating (Housley et al. 1997; Richards 2003) but also by the phylogeographic evidence provided by mtDNA haplogroup V (Torroni et al. 1998; 2001a) and Y-chromosome haplogroups R1b and I1b2 (Semino et al. 2000; Cinniog˘ lu et al. 2004; Rootsi et al. 2004).

Among the mtDNA haplogroups of Europe, haplogroup H displays two unique features: an extremely wide geographic distribution and a very high frequency in most of its range. Indeed, it is by far the most prevalent haplogroup in all European populations except the Saami, is very common in North Africa and the Middle East, and retains frequencies of 5%–10% even in northern India and Central Asia, at the edges of its distribution range (Richards et al. 2002).

Previous studies have proposed that haplogroup H (i) originated in the Middle East ~30–25 kya; (ii) expanded into Europe in association with a second Paleolithic wave, possibly contemporary with the diffusion of the Gravettian technology (25–20 kya); and (iii) was strongly involved in the late-glacial expansions from iceage refugia after the LGM (Torroni et al. 1998; Richards et al. 2000). In addition, because of its high frequency and wide distribution, haplogroup H most likely participated in all subsequent episodes of putative gene flow in western Eurasia, such as the Neolithic diffusion of agriculture from the Near East, the expansion of the Kurgan culture from southern Ukraine, and the recent events of gene flow to northern India.